Simon Biddie
@SimonBiddie
Clinical Academic, Intensive Care Medicine
New paper out in Genome Biology! 🎉 We lay out best-practice guidelines for releasing variant effect predictors, developed through the Atlas of Variant Effects Alliance @varianteffects Open, interpretable, and clinically useful VEPs are the goal. 📄 doi.org/10.1186/s13059…
In our latest study with @jmarshlab, we extend our work on phenotype-level molecular mechanism prediction. Read more here: biorxiv.org/content/10.110…
Proteome-Scale Prediction of Molecular Mechanisms Underlying Dominant Genetic Diseases @BdonyiMihly -> Predict whether human protein coding genes to be associated with DN,GOF,or LOF molecular disease mechanisms. 💻Code: osf.io/z4dcp 📜Paper: doi.org/10.1371/journa…
Introducing scE2G: a new model to link enhancers to target genes using single-cell data. Excited that scE2G will enable building enhancer maps in hundreds of cell types in the human body! Wonderful collaboration with @robin_andersson @613weilin @mayayayas and others 👇
Excited to share our latest preprint on scE2G – a new model to link enhancers to target genes using single-cell data – with state-of-the-art performance across multiple perturbation benchmarks. biorxiv.org/cgi/content/sh… Read more below! 1/12
Diverse and interdisciplinary projects suitable to many backgrounds, in projects that develop skills important for the future of biomedical sciences. If you are interested in protein structure prediction, DNA and disease, please get in touch with myself or @jmarshlab
Excited to share our latest preprint on scE2G – a new model to link enhancers to target genes using single-cell data – with state-of-the-art performance across multiple perturbation benchmarks. biorxiv.org/cgi/content/sh… Read more below! 1/12
Just published in @PLOSGenetics. @LucianaGA84 @EliasFriman @Phlya show surprising differences in what 3C- and imaging-based methods tell us about enhancer-promoter communication. @mrc_hgu @EdinUni_IGC journals.plos.org/plosgenetics/a… ed.ac.uk/institute-gene…
I am so very proud of @charles_bell92 and this manuscript from @TheDawsonLab @PeterMacRes - A labour of love driven by curiosity, resilience and incredible teamwork over many years. We hope it contributes substantially to our field nature.com/articles/s4158…
Kudos again to the team @genomewizard, Sergi Sayols, @Diana_Ktn, @belilab, protein production and genomics IMB facilities @IMB @sfb1361
Vassilis Roukos' team developed BreakTag, a method to assess the location & structure of #DNA double-strand breaks made by #CRISPR/Cas9. It helps scientists design better genome editing tools to treat genetic diseases. ➡️imb.de/about-imb/news… Full paper at @NatureBiotech
We’re recruiting for multiple positions in my lab in New York and Stockholm, at MSc and PhD levels. If you’re interested in pursuing creative systems genetics questions with tools/data like Developmental GTEx, CRISPR and single-cell, please read further / share. 1/
Link to article on our website: ed.ac.uk/institute-gene… Full paper here: science.org/doi/10.1126/sc…
Want to learn about cell death and tissue fibrosis following lung injury? We have a @pathsoc funded PhD position available with myself, @davidadorward @prakramacha supervising. Hugely supportive environment @EdinUni_IRR. Info: rb.gy/lm0xbb please RT!
Important we all keep highlighting this issue and calling for the needed action to address the crisis. Thanks @LordsSTCom for continuing to do so!
New data published by @ukmedschools shows a continuing, and concerning, decline in clinical academics. At the start of 2023, we published our letter to the Government sounding the alarm about this issue. medschools.ac.uk/news/investmen… Letter: committees.parliament.uk/publications/3…
🚨Are you a UK medical student? Your colleagues are gathering the views of medical students about the announced SFP changes. To be able to represent the student community, they need as many people as possible to complete the survey. Please take a look 👇 forms.office.com/e/TGykFuE0fJ